To the uninitiated, it might seem almost paradoxical that such an outwardly humble substance as soil should bear such advanced technical treatments as those presented here: microarrays, reporter genes, molecular probes, fluorescence microscopy, metagenomics, proteomics, and others. However, soil microbial communities are arguably among the most complex biological entities, dwelling in extremely heterogeneous and complex physical environments. The study of plant-associated microbial communities presents challenges similar to those encountered in soils. Environmental microbiology is a dynamic field that has produced many innovations in recent decades. A section presents both classical and cutting-edge techniques in an attempt to summarize the current state of the field.